🧬 🦠 🏙️ Urban vs rural lifestyles create dramatically different gut microbiomes. But how do these different gut microbiomes affect the host? Excited to share our new paper: www.biorxiv.org/content/10.1...

⚠️ Be aware! There are phishing websites for commonly used bioinformatics tools! ⚠️ Samtools and minimap2 affected, but it's likely just the tip of the iceberg. Be careful to use only official sources for your downloads, and let your colleagues and lab members know. #bioinformatics #microsky

Are you a scientist who speaks Italian? Consider joining this initiative that connects scientists with elementary or middle school students in Italy through monthly correspondence ✒️

If you generate or reuse #microbiome data, check out these guidelines for equitable sequence data reuse. Grateful to @alexjprobst.bsky.social and his team for leading this important work and for bringing together 160+ microbiome scientists (myself included) to contribute! doi.org/10.1038/s415...

Our article on equitable reuse of public sequencing data is out! Led by @alexjprobst.bsky.social, @lhug.bsky.social, Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and myself -, co-authored by Anke Heyder, and developed in consultation with 167 scientists. tinyurl.com/n6yeanmk

My commentary article, featuring the work of Aasmets et al. on the long-lasting effects of medications on the gut microbiome, is now out in mSystems @asm.org #microbiome #microsky doi.org/10.1128/msys...

Full thread will come later, but @annacusco.bsky.social's preprint on the dog pet gut microbiome is out! Using ONT+Illumina, we get better MAGs than to corresponding species representative in public databases doi.org/10.1101/2025...

DYK that mothers' milk has a circadian rhythm, providing dynamic signals to baby? 🤱🏻🕧🕐 New study shows: - Cortisol peaks in early am ('wake up!' 😀) - Melatonin peaks late at night ('sleepy time' 😴) Moms who pump may want to label & feed am/pm milk separately. www.frontiersin.org/journals/nut...

Really timely and important work to tackle global #honeybee population decline: 🐝 Engineered yeast provides rare but essential pollen sterols for honeybees www.nature.com/articles/s41... @philstevenson.bsky.social

Manually curated and harmonized metadata for over 110k metagenomic samples! (58k samples from the human gut alone!)🦠 Proud to have contributed to Metalog, the latest @borklab.bsky.social resource: www.biorxiv.org/content/10.1... #microsky #microbiome

We hope many of you will find it useful, and will continue to add data. Here's the preprint: www.biorxiv.org/content/10.1... - hopefully coming soon to a NAR Database Issue near you 😅 Thanks to everyone in the @borklab.bsky.social @embl.org who contributed to this! 7/7

We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7 #microsky

Last year, I joined a brilliant group of researchers for a 3-week deep dive into host–microbe systems. Each week explored a different theme, led by inspiring lecturers. I’m excited to share that videos of their talks — along with presentations by several team members — are now on YouTube:

Theory of host-microbe symbioses: Challenges & opportunities Discussion on mathematical modeling of microbial symbioses with 3 noted areas requiring advancement: nested ecology w/in host or holobiont, holobiont population dynamics & symbiont-mediated speciation www.cell.com/cell-host-mi...

Our article on the challenges and opportunities in studying host-microbe symbioses is now published in Cell Host & Microbe! @cp-cellhostmicrobe.bsky.social www.sciencedirect.com/science/arti...

The team's first preprint is out! Led by ‪ ‪@vishnuprasoodanan.bsky.social‬‬ & @omaistrenko.bsky.social , we asked a question (almost) as old as microbiology: how many prokaryotic species exist on Earth? More specifically, how much diversity is "hiding" in existing metagenomic data? A 🧵.

There are many more stories in the preprint, so go ahead and read it: www.biorxiv.org/content/10.1... We welcome feedback!

For #worldmicrobiomeday, re-sharing our recent Review by @pamferretti.bsky.social, Kelsey Johnson, @sambhawa.bsky.social & @blekhman.bsky.social on the 'Genomics of host–microbiome interactions in humans', which is free to read using this link: rdcu.be/etIRy

Excited to share our new article exploring the eukaryotic diversity and composition in the gut microbiome of wild baboons! doi.org/10.1186/s425...

📢New Publication Alert 📢 I’m proud to share a major milestone in my PhD journey. My first paper has officially been published: “Eukaryotic composition across seasons and social groups in the gut microbiota of wild baboons”. animalmicrobiome.biomedcentral.com/articles/10....

Just out in Nature Reviews Genetics! From twin studies to microbiome GWAS to cutting-edge transcriptomics, we explore the cross-talk between our genes and the microbiome! Fun working together with @pamferretti.bsky.social @blekhman.bsky.social Kelsey Johnson www.nature.com/articles/s41...

Had a lot of fun writing this with three amazing postdocs -- Pamela Ferretti @pamferretti.bsky.social, Sambhawa Priya @sambhawa.bsky.social, and Kelsey Johnson See this thread from Pamela highlighting some key points from our review: bsky.app/profile/pamf...

📣 Happy to share our review on host-microbiome genomics! We synthesize the growing field exploring interactions between human genetics and the microbiome, building a roadmap for mapping the dialogue between our genes and microbes Out now in Nature Reviews Genetics👇 www.nature.com/articles/s41...

Interested in microbiome GWAS and heritability studies? Check out our new Review in Nature Reviews Genetics! We explore key findings, challenges, and future directions of the field. rdcu.be/epoRR @blekhman.bsky.social @sambhawa.bsky.social and Dr. Kelsey Johnson.

Genomics of host–microbiome interactions in humans www.nature.com/articles/s41... #jcampubs

New online! Genomics of host–microbiome interactions in humans

🚨 Out now! Chronostrain - a method to profile low abundance strains in longitudinal microbiome samples 🦠💻 @travis.gibsonlab.io @younhk.bsky.social @gibsonlab.io @harvardmed.bsky.social @broadinstitute.org #MicroSky 🦠 #MicrobiomeSky www.nature.com/articles/s41...

We wrote up the process we've developed for processing microbiome data in bulk! Workflow management tools are miraculous for processing a project with lots of samples, but when you have lots of *projects* too, as we do when pulling data from NCBI databases, it gets hard to juggle. #microbiomesky

Excited to share the Compendium Manager -- our new tool for scaling bioinformatics pipelines! Launch thousands of analyses, track progress, and maintain reproducibility. Developed by @richabdill.com. Check it out: arxiv.org/abs/2505.11385

Do people in the same household share strains when they have the same species? How many cells transmit when a strain is shared? Can strain composition be dynamic when species composition is stable? We answer these and related questions for the facial skin microbiome in our latest paper. 🧵[1/10]

Excited to share our latest work on the gut microbiome in inflammatory bowel disease patients. This is the result of hard work across generations of trainees in the Donia Lab, in collaboration with amazing scientists (Nobuhiko Kamada and Lea Ann Chen). www.cell.com/cell-host-mi...

Last week @richabdill.com and @samanthagraham.bsky.social's paper was featured on the cover of Cell! The cover, portraying microbes on shelves shaped like a world map, was possible thanks to the amazing team of illustrators at SciStories ✏️🦠

These are challenging times for science, but I'm happy to share a bright moment: our work is on the cover of Cell today. We built a compendium of human gut microbiomes integrating 168K worldwide samples, revealing patterns of microbiome variation across the globe www.cell.com/cell/current...

Excited to this out in Cell! Check out @samanthagraham.bsky.social's thread for the key findings of this massive effort to uniformly analyze 168k human gut amplicon samples! @richabdill.com @blekhman.bsky.social

Use the Human Microbiome Compendium data! We made the data and code available, & created a website and R package to navigate the compendium. Links: - Website: microbiomap.org - Data: zenodo.org/records/1373... - R package: blekhmanlab.github.io/MicroBioMap/ - Code: github.com/blekhmanlab/...

Today we report a new compendium of human gut microbiomes with >168,000 samples By analyzing this massive dataset, we discovered distinct microbiome patterns across the globe, and show we can predict where a person lives just from their gut bacteria Now out in Cell: www.cell.com/cell/fulltex...

I'm very happy to report that Matt Schechter's PhD work is now online as a pre-print: "Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities", www.biorxiv.org/content/10.1... Here's a little 🧵 about it.

1/ 🚨 New preprint alert! 🚨 We’re thrilled to share our latest work exploring microbiome & genomic #Bifidobacterium co-evolutionary & functional signatures across diverse animal hosts. This has been a long time coming, & huge credit to Magda for her incredible hard work as first author! 🐾✨👇

New year, new lab logo! Designed by talented lab members @pamferretti.bsky.social, @richabdill.com, and Sabrina Arif

Wild animal microbiome community, assemble! I hope to see many more people joining this starter pack, let me know if you would like to be included! go.bsky.app/LXjWaJq

Excited to see this out in Cell! If you use microbiome data to look for disease associations, you might want to make sure microbial load is not confounding your results! www.cell.com/cell/fulltex... Congratulations @suguru-nishijima.bsky.social @borklab.bsky.social and others #microsky #microbiome

Two important papers on the gut microbiome and disease —The fecal microbial load is a key determinant confounding prior reports of association with diseases cell.com/cell/fulltex... —Innovative approaches to establish causality and mechanisms science.org/doi/10.1126/...

EMBL's press release: www.embl.org/news/science...

If you have human gut microbiome data (metagenomics or 16S), you can use our tool at microbiome-tools.embl.de/mlp/ to predict cell counts, so that you can find out if any microbiome changes in your study population are actually driven by changes in bacterial cell counts

Hot off the press: "Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations" www.sciencedirect.com/science/arti... See below for @suguru-nishijima.bsky.social 's thread on the preprint! #microsky #microbiome

Excited to share our latest preprint on a novel computational tool to predict fecal microbial load solely from relative species profiles! Our study revealed that fecal microbial load is a substantial confounder in microbiome-disease association studies. www.biorxiv.org/content/10.1...

Intense and very productive week attending #cshlmbiome! I particularly loved the amount of novel results presented at talks and posters, and the very collaborative environment...this should be the norm! 👆 Kudos to the organizers for this fantastic meeting! #microbiome

Our metagenome profiler sylph is now published in Nature Biotechnology! (www.nature.com/articles/s41...)

Mother's milk is often the sole source of nutrition for the baby. Milk also contains diverse bacterial communities -- but how to these bacteria impact the infant gut microbiome? Our latest: www.biorxiv.org/content/10.1...